if you have ther batteries hooked together, it will charge the one that needs it. Or get an isolator.
That’s not always true. I run into this on boats alot. If you have them both connected together and one is fully charged and the other is not, the regulator will not know that the other batt needs more amps unless the batt’s are connected to the alt by them selves. It only see's the fuller charged batt. Eventually the fact that they are connected all the time, the full batt will bleed off amps to the lower charged batt. This is a process that could take several days depending. I recently had this problem on my boat with 2 batts, one was fully charged and the other was near dead. My problem was I use a switch to select the batt I want to use. This switch has the option of selecting both at the same time. I thought if I ran the boat for a couple of hours with both batts on, this way it would charge both but I read now that it won't not to mention my anchor batt died in a matter of a couple of hours running the radio. It charges the batt that is fuller and then thinks it's job is done and pulls back amps. My boat uses an alt just the same as a car by the way. If you are going to leave both always connected at the same time all the time, make sure both have a lead from the alt this will help the chances that both batts will be charged. Just make sure they are both fully charged when you install them and are the same size batts, this will help make sure they both receive the same amount of charging. Also make sure that both batt's have a lead to the ACC so you are not trying to draw from one batt to another. Drawing from one batt to another is really inefficient because it will deplete the first batt closest to the ACC post as they are wired before drawing on the batt further away. Hope this makes sense lol.